Posts by life99945

... Hi!
I mapped paired end library to a genome. Now I am trying to visualise it via IGV, but I am always getting this message when trying to jump to a certain chromosome: Error encountered querying alignments: java.lang.NullPointerException. Reference genome have 19 chromosomes and a lot of unplaced g ...

... Hi,
I have paired end reads which I mapped to a reference genome. This genome contains two types of contigs.
First are contigs with NC identifiers, which represent chromosomes and second type are contigs with NW(NW_XXXXXX) identifiers, which should be supercontigs with gaps.
The questions are:
W ...

... I just realized that Tablet divided my genome into chromosomes when I looked at 3-d column of the sam file and I can see location of the reads! Thank you!
p.s. I think order of read fragments is correct, otherwise bwa said that he can not find the second pair and interrupted the process.
...

... Thank you for the answer!
If this is the case, then the problem of incorrectly paired sequences disappears. However I still can’t understand on which specific part of the genome the insert was aligned. I tried to visualise with ncbi sequence viewer and IGV and it shows nothing. Only Tablet shows m ...

... Hi!
I have a library of paired BAC end sequences, ~800bp each. Expected insertion length is 150kb. After mapping it to a reference genome I visualised results with Tablet program.
The issue is that almost all of my sequences said to be "improperly paired' but despite that Tablet shows an insert l ...

... As far as I understand what they were doing in that article is that from the pair of sequences with identity >=95% they were filtering out the shorter ones, but they didn't have reference genome, so maybe I don't need to do that.
There is one moment that I don't quite understend: shouldn't i ha ...